├── .gitignore ├── Auxiliary.cpp ├── Auxiliary.h ├── Bitmapper_main.cpp ├── Dockerfile ├── Index.cpp ├── Index.h ├── LICENSE ├── Levenshtein_Cal.cpp ├── Levenshtein_Cal.h ├── Makefile ├── Process_CommandLines.cpp ├── Process_CommandLines.h ├── Process_Reads.cpp ├── Process_Reads.h ├── Process_sam_out.cpp ├── Process_sam_out.h ├── README.md ├── Ref_Genome.cpp ├── Ref_Genome.h ├── SAM_queue.cpp ├── SAM_queue.h ├── Schema.cpp ├── Schema.h ├── bam_prase.cpp ├── bam_prase.h ├── bwt.cpp ├── bwt.h ├── htslib ├── INSTALL ├── LICENSE ├── Makefile ├── NEWS ├── README ├── aclocal.m4 ├── bcf_sr_sort.c ├── bcf_sr_sort.h ├── bgzf.c ├── bgzip.1 ├── bgzip.c ├── config.mk.in ├── configure.ac ├── cram │ ├── cram.h │ ├── cram_codecs.c │ ├── cram_codecs.h │ ├── cram_decode.c │ ├── cram_decode.h │ ├── cram_encode.c │ ├── cram_encode.h │ ├── cram_external.c │ ├── cram_index.c │ ├── cram_index.h │ ├── cram_io.c │ ├── cram_io.h │ ├── cram_samtools.c │ ├── cram_samtools.h │ ├── cram_stats.c │ ├── cram_stats.h │ ├── cram_structs.h │ ├── files.c │ ├── mFILE.c │ ├── mFILE.h │ ├── misc.h │ ├── open_trace_file.c │ ├── open_trace_file.h │ ├── os.h │ ├── pooled_alloc.c │ ├── pooled_alloc.h │ ├── rANS_byte.h │ ├── rANS_static.c │ ├── rANS_static.h │ ├── sam_header.c │ ├── sam_header.h │ ├── string_alloc.c │ └── string_alloc.h ├── errmod.c ├── faidx.5 ├── faidx.c ├── hfile.c ├── hfile_gcs.c ├── hfile_internal.h ├── hfile_libcurl.c ├── hfile_net.c ├── hfile_s3.c ├── hts.c ├── hts_internal.h ├── hts_os.c ├── htsfile.1 ├── htsfile.c ├── htslib.mk ├── htslib.pc.in ├── htslib │ ├── bgzf.h │ ├── cram.h │ ├── faidx.h │ ├── hfile.h │ ├── hts.h │ ├── hts_defs.h │ ├── hts_endian.h │ ├── hts_log.h │ ├── hts_os.h │ ├── kbitset.h │ ├── kfunc.h │ ├── khash.h │ ├── khash_str2int.h │ ├── klist.h │ ├── knetfile.h │ ├── kseq.h │ ├── ksort.h │ ├── kstring.h │ ├── regidx.h │ ├── sam.h │ ├── synced_bcf_reader.h │ ├── tbx.h │ ├── thread_pool.h │ ├── vcf.h │ ├── vcf_sweep.h │ └── vcfutils.h ├── htslib_vars.mk ├── kfunc.c ├── knetfile.c ├── kstring.c ├── m4 │ └── hts_prog_cc_warnings.m4 ├── md5.c ├── multipart.c ├── os │ ├── lzma_stub.h │ └── rand.c ├── plugin.c ├── probaln.c ├── realn.c ├── regidx.c ├── sam.5 ├── sam.c ├── synced_bcf_reader.c ├── tabix.1 ├── tabix.c ├── tbx.c ├── test │ ├── auxf#values.sam │ ├── auxf#values_java.cram │ ├── auxf.fa │ ├── auxf.fa.fai │ ├── bgziptest.txt │ ├── bgziptest.txt.gz │ ├── bgziptest.txt.gz.gzi │ ├── c1#bounds.sam │ ├── c1#clip.sam │ ├── c1#noseq.sam │ ├── c1#pad1.sam │ ├── c1#pad2.sam │ ├── c1#pad3.sam │ ├── c1#unknown.sam │ ├── c1.fa │ ├── c1.fa.fai │ ├── c2#pad.sam │ ├── c2.fa │ ├── c2.fa.fai │ ├── ce#1.sam │ ├── ce#1000.sam │ ├── ce#2.sam │ ├── ce#5.sam │ ├── ce#5b.sam │ ├── ce#5b_java.cram │ ├── ce#large_seq.sam │ ├── ce#supp.sam │ ├── ce#tag_depadded.sam │ ├── ce#tag_padded.sam │ ├── ce#unmap.sam │ ├── ce#unmap1.sam │ ├── ce#unmap2.sam │ ├── ce.fa │ ├── ce.fa.fai │ ├── compare_sam.pl │ ├── cross_validate.sh │ ├── faidx.fa │ ├── fastqs.fq │ ├── fastqs_README.txt │ ├── fieldarith.c │ ├── fieldarith.sam │ ├── formatcols.vcf │ ├── formatmissing-out.vcf │ ├── formatmissing.vcf │ ├── hfile.c │ ├── hts_endian.c │ ├── md#1.sam │ ├── md.fa │ ├── md.fa.fai │ ├── mpileup │ │ ├── c1#pad1.out │ │ ├── c1#pad1.sam │ │ ├── c1#pad2.out │ │ ├── c1#pad2.sam │ │ ├── c1#pad3.out │ │ ├── c1#pad3.sam │ │ ├── mp_D.out │ │ ├── mp_D.sam │ │ ├── mp_DI.out │ │ ├── mp_DI.sam │ │ ├── mp_I.out │ │ ├── mp_I.sam │ │ ├── mp_ID.out │ │ ├── mp_ID.sam │ │ ├── mp_N.out │ │ ├── mp_N.sam │ │ ├── mp_N2.out │ │ ├── mp_N2.sam │ │ ├── mp_P.out │ │ ├── mp_P.sam │ │ ├── mpileup.tst │ │ └── test-pileup.sh │ ├── noroundtrip-out.vcf │ ├── noroundtrip.vcf │ ├── pileup.c │ ├── range.bam │ ├── range.bam.bai │ ├── range.cram │ ├── range.cram.crai │ ├── range.out │ ├── realn01.fa │ ├── realn01.fa.fai │ ├── realn01.sam │ ├── realn01_exp-a.sam │ ├── realn01_exp-e.sam │ ├── realn01_exp.sam │ ├── realn02-r.sam │ ├── realn02.fa │ ├── realn02.fa.fai │ ├── realn02.sam │ ├── realn02_exp-a.sam │ ├── realn02_exp-e.sam │ ├── realn02_exp.sam │ ├── sam.c │ ├── simple_test_driver.sh │ ├── tabix │ │ ├── bed_file.Y.100200.out │ │ ├── bed_file.bed │ │ ├── gff_file.X.2934832.2935190.out │ │ ├── gff_file.gff │ │ ├── large_chr.20.1.2147483647.out │ │ ├── large_chr.vcf │ │ ├── tabix.tst │ │ ├── test-tabix.sh │ │ ├── vcf_file.1.3000151.out │ │ ├── vcf_file.2.3199812.out │ │ └── vcf_file.vcf │ ├── test-bcf-sr.c │ ├── test-bcf-sr.pl │ ├── test-bcf-translate.c │ ├── test-bcf-translate.out │ ├── test-logging.pl │ ├── test-regidx.c │ ├── test-vcf-api.c │ ├── test-vcf-api.out │ ├── test-vcf-hdr-in.vcf │ ├── test-vcf-hdr.out │ ├── test-vcf-sweep.c │ ├── test-vcf-sweep.out │ ├── test.pl │ ├── test_bgzf.c │ ├── test_kstring.c │ ├── test_realn.c │ ├── test_view.c │ ├── thrash_threads1.c │ ├── thrash_threads2.c │ ├── thrash_threads3.c │ ├── thrash_threads4.c │ ├── thrash_threads5.c │ ├── thrash_threads6.c │ ├── thrash_threads7.c │ ├── thread_pool.md │ ├── xx#MD.sam │ ├── xx#MD2.sam │ ├── xx#blank.sam │ ├── xx#large_aux.sam │ ├── xx#large_aux2.sam │ ├── xx#large_aux_java.cram │ ├── xx#minimal.sam │ ├── xx#pair.sam │ ├── xx#repeated.sam │ ├── xx#rg.sam │ ├── xx#tlen.sam │ ├── xx#tlen2.sam │ ├── xx#triplet.sam │ ├── xx#unsorted.sam │ ├── xx.fa │ └── xx.fa.fai ├── textutils.c ├── textutils_internal.h ├── thread_pool.c ├── thread_pool_internal.h ├── vcf.5 ├── vcf.c ├── vcf_sweep.c ├── vcfutils.c └── version.sh ├── ksw.cpp ├── ksw.h ├── libdivsufsort-2.0.1 ├── AUTHORS ├── CMakeLists.txt ├── CMakeModules │ ├── AppendCompilerFlags.cmake │ ├── CheckFunctionKeywords.cmake │ ├── CheckLFS.cmake │ ├── ProjectCPack.cmake │ └── cmake_uninstall.cmake.in ├── COPYING ├── ChangeLog ├── ChangeLog.old ├── INSTALL ├── Makefile.am ├── Makefile.in ├── NEWS ├── README ├── VERSION ├── aclocal.m4 ├── config │ ├── config.guess │ ├── config.sub │ ├── depcomp │ ├── install-sh │ ├── ltmain.sh │ └── missing ├── configure ├── configure.ac ├── examples │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── Makefile.in │ ├── bwt.c │ ├── mksary.c │ ├── sasearch.c │ ├── suftest.c │ └── unbwt.c ├── include │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── Makefile.in │ ├── config.h.cmake │ ├── config.h.in │ ├── divsufsort.h.cmake │ ├── divsufsort64.h.in │ ├── divsufsort_private.h │ └── lfs.h.cmake ├── lib │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── Makefile.in │ ├── divsufsort.c │ ├── libdivsufsort.sym │ ├── libdivsufsort64.sym │ ├── sssort.c │ ├── trsort.c │ └── utils.c ├── m4 │ ├── libtool.m4 │ ├── ltoptions.m4 │ ├── ltsugar.m4 │ ├── ltversion.m4 │ └── lt~obsolete.m4 └── pkgconfig │ ├── CMakeLists.txt │ └── libdivsufsort.pc.cmake ├── pSAscan-0.1.0 ├── AUTHORS ├── LICENCE ├── README ├── VERSION ├── src │ ├── Makefile │ ├── main.cpp │ └── psascan_src │ │ ├── approx_rank.h │ │ ├── async_backward_skip_stream_reader.h │ │ ├── async_bit_stream_writer.h │ │ ├── async_multifile_bit_stream_reader.h │ │ ├── async_stream_writer.h │ │ ├── async_vbyte_stream_reader.h │ │ ├── background_block_reader.h │ │ ├── background_chunk_reader.h │ │ ├── bitvector.h │ │ ├── bwt_merge.h │ │ ├── compute_gap.h │ │ ├── compute_left_gap.h │ │ ├── compute_right_gap.h │ │ ├── distributed_file.h │ │ ├── em_compute_initial_ranks.h │ │ ├── gap_array.h │ │ ├── gap_buffer.h │ │ ├── half_block_info.h │ │ ├── inmem_psascan_src │ │ ├── bwtsa.h │ │ ├── change_gt_reference_point.h │ │ ├── compute_initial_gt_bitvectors.h │ │ ├── divsufsort_template.h │ │ ├── initial_partial_sufsort.h │ │ ├── inmem_bwt_from_sa.h │ │ ├── inmem_bwtsa_merge.h │ │ ├── inmem_compute_gap.h │ │ ├── inmem_compute_initial_ranks.h │ │ ├── inmem_gap_array.h │ │ ├── inmem_psascan.h │ │ ├── inmem_stream.h │ │ ├── inmem_update.h │ │ ├── merge_schedule.h │ │ ├── pagearray.h │ │ ├── parallel_copy.h │ │ ├── parallel_expand.h │ │ ├── parallel_merge.h │ │ ├── parallel_shrink.h │ │ ├── rank.h │ │ ├── sparse_isa.h │ │ └── srank_aux.h │ │ ├── merge.h │ │ ├── multifile.h │ │ ├── multifile_bit_stream_reader.h │ │ ├── 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